1-41511257-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_024503.5(HIVEP3):​c.6415G>A​(p.Glu2139Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000442 in 1,602,634 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 5 hom. )

Consequence

HIVEP3
NM_024503.5 missense

Scores

2
16

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.612
Variant links:
Genes affected
HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.003950864).
BP6
Variant 1-41511257-C-T is Benign according to our data. Variant chr1-41511257-C-T is described in ClinVar as [Benign]. Clinvar id is 3035562.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HIVEP3NM_024503.5 linkuse as main transcriptc.6415G>A p.Glu2139Lys missense_variant 9/9 ENST00000372583.6
HIVEP3NM_001127714.3 linkuse as main transcriptc.6412G>A p.Glu2138Lys missense_variant 8/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HIVEP3ENST00000372583.6 linkuse as main transcriptc.6415G>A p.Glu2139Lys missense_variant 9/91 NM_024503.5 P5Q5T1R4-1
HIVEP3ENST00000372584.5 linkuse as main transcriptc.6412G>A p.Glu2138Lys missense_variant 8/81 A2Q5T1R4-2
HIVEP3ENST00000643665.1 linkuse as main transcriptc.6412G>A p.Glu2138Lys missense_variant 8/8 A2Q5T1R4-2
HIVEP3ENST00000460604.1 linkuse as main transcriptn.1342G>A non_coding_transcript_exon_variant 5/52

Frequencies

GnomAD3 genomes
AF:
0.00225
AC:
342
AN:
152114
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00741
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.000678
AC:
162
AN:
238854
Hom.:
0
AF XY:
0.000488
AC XY:
63
AN XY:
129112
show subpopulations
Gnomad AFR exome
AF:
0.00836
Gnomad AMR exome
AF:
0.000384
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000279
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000465
Gnomad OTH exome
AF:
0.000512
GnomAD4 exome
AF:
0.000253
AC:
367
AN:
1450402
Hom.:
5
Cov.:
33
AF XY:
0.000190
AC XY:
137
AN XY:
719958
show subpopulations
Gnomad4 AFR exome
AF:
0.00777
Gnomad4 AMR exome
AF:
0.000521
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000200
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000995
Gnomad4 OTH exome
AF:
0.000835
GnomAD4 genome
AF:
0.00225
AC:
342
AN:
152232
Hom.:
1
Cov.:
32
AF XY:
0.00214
AC XY:
159
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.00739
Gnomad4 AMR
AF:
0.00176
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.000411
Hom.:
0
Bravo
AF:
0.00272
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00682
AC:
30
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000759
AC:
92

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

HIVEP3-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesDec 09, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.50
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
20
DANN
Uncertain
0.98
DEOGEN2
Benign
0.12
.;T;.
Eigen
Benign
-0.16
Eigen_PC
Benign
-0.081
FATHMM_MKL
Benign
0.68
D
LIST_S2
Benign
0.84
.;T;T
MetaRNN
Benign
0.0040
T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.1
.;M;.
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.47
T
PROVEAN
Benign
-0.83
.;N;N
REVEL
Benign
0.051
Sift
Benign
0.032
.;D;D
Sift4G
Benign
0.090
.;T;T
Polyphen
0.64
P;P;P
Vest4
0.090, 0.13
MVP
0.28
MPC
0.25
ClinPred
0.015
T
GERP RS
3.7
Varity_R
0.14
gMVP
0.17

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs148581312; hg19: chr1-41976928; COSMIC: COSV56018560; API